Comparative DNA analysis across diverse genomes

We review concepts and methods for comparative analysis of complete genomes including assessments of genomic compositional contrasts based on dinucleotide and tetranucleotide relative abundance values, identifications of rare and frequent oligonucleotides, evaluations and interpretations of codon biases in several large prokaryotic genomes, and characterizations of compositional asymmetry between the two DNA strands in certain bacterial genomes. The discussion also covers means for identifying alien (e.g. laterally transferred) genes and detecting potential specialization islands in bacterial genomes.

Codon usages in different gene classes of the Escherichia coli genome

A new measure for assessing codon bias of one group of genes with respect to a second group of genes is introduced. In this formulation, codon bias correlations for Escherichia coli genes are evaluated for level of expression, for contrasts along genes, for genes in different 200 kb (or longer) contigs around the genome, for effects of gene size, for variation over different function classes, for codon bias in relation to possible lateral transfer and for dicodon bias for some gene classes. Among the function classes, codon biases of ribosomal proteins are the most deviant from the codon frequencies of the average E. coli gene. Other classes of 'highly expressed genes' (e.g. amino acyl tRNA synthetases, chaperonins, modification genes essential to translation activities) show less extreme codon biases. Consistently for genes with experimentally determined expression rates in the exponential growth phase, those of highest molar abundances are more deviant from the average gene codon frequencies and are more similar in codon frequencies to the average ribosomal protein gene. Independent of gene size, the codon biases in the 5' third of genes deviate by more than a factor of two from those in the middle and 3' thirds. In this context, there appear to be conflicting selection pressures imposed by the constraints of ribosomal binding, or more generally the early phase of protein synthesis (about the first 50 codons) may be more biased than the complete nascent polypeptide. In partitioning the E. coli genome into 10 equal lengths, pronounced differences in codon site 3 G+C frequencies accumulate. Genes near to oriC have 5% greater codon site 3 G+C frequencies than do genes from the ter region. This difference also is observed between small (100-300 codons) and large (>800 codons) genes. This result contrasts with that for eukaryotic genomes (including human, Caenorhabditis elegans and yeast) where long genes tend to have site 3 more AT rich than short genes. Many of the above results are special for E. coli genes and do not apply to genes of most bacterial genomes. A gene is defined as alien (possibly horizontally transferred) if its codon bias relative to the average gene exceeds a high threshold and the codon bias relative to ribosomal proteins is also appropriately high. These are identified, including four clusters (operons). The bulk of these genes have no known function.

Evaluation for an observation effect in a prospective cohort study of oral health outcomes

OBJECTIVES

Evaluation for changes in behavior due to research participants' knowledge that behavior is being observed (also referred to as a Hawthorne effect or reactivity) has received little attention in the dental literature. The Florida Dental Care Study, a prospective, non-randomized, longitudinal study of oral health outcomes, provides some inferential power to evaluate for an effect on dental care use due to participants' knowledge that this behavior was being observed. The purpose of this paper is to document that an observation effect can occur in dental studies, and to estimate its magnitude in four groups that were defined by their typical approach to dental care as stated at baseline: consistent regular attenders (CRAs); inconsistent regular attenders (IRAs); consistent problem-oriented attenders (CPOAs); and inconsistent problem-oriented attenders (IPOAs).

METHODS

At baseline, 873 respondents with at least one natural tooth and who were 45 years of age or older participated for an interview and clinical dental examination. Respondents were asked about their dental care use in general and check-up use in particular at 6-month intervals over a period of 24 months.

RESULTS

Dental care use in general and check-up use in particular varied across time points and across the four groups of the sample. There was some stimulation in dental care use for the sample overall, but by the 18-to-24-month period, use had returned to baseline levels. In a direction opposite from that hypothesized, results from the CRAs suggested decreased use of dental care over the course of the 24 months of observation. No consistent pattern was evident for the IRAs, CPOAs, or IPOAs.

CONCLUSIONS

An observation effect was evident, but was modest in magnitude and differed within and between sub-groups of the sample. While self-selection into dental care user groups is an expected and desirable feature of this design, the size of the user/non-user groups was affected for some subgroups. We conclude that dental care studies with the potential for an observation effect should evaluate for this effect by distinguishing sub-groups of the sample based on their propensity (as stated at baseline) to use dental care. These differential effects across sub-groups should be taken into account as inferences are made.

Inhibition of mediator release from dispersed nasal polyp cells by cyclosporin A

The mechanisms of action of cyclosporin A require further elucidation since this drug includes anti-inflammatory properties unrelated to its previously documented effect of T cells. A study was performed using enzymatically dispersed cells from nasal polyps of 7 subjects to examine the effects of cyclosporin A on the release of histamine, leukotriene C4/D4 (LTC4/D4) and thromboxane (TxB2) following stimulation by anti-IgE. Cells were resuspended and preincubated with cyclosporin A (0.1, 1 and 10 microM) or 0.1% DMSO (the vehicle used to dissolve cyclosporin A) for 20 min prior to challenge with 10 microgram/ml epsilon-chain-specific anti-IgE for 45 min at 37 degrees C. Histamine, LTC4/D4 and TxB2 were measured using EIA. Cyclosporin A significantly inhibited the release of histamine, LTC4/D4, and TxB2 in a concentration-dependent manner. IC30 values, histamine (5.1 microM), LTC4/D4 (7.8 microM) and TxB2 (6.2 microM), were determined. These data demonstrate new antiallergic properties of cyclosporin A using a novel in vitro model which mimics more closely allergic inflammation.

Expression of the high-affinity receptor for IgE on bronchial epithelial cells of asthmatics

Bronchial epithelial cells are the first cells to come into contact with inhaled pneumoallergens. It has been suggested that these cells may play an important role in the allergic response, and indeed bronchial epithelial cells of some atopic asthmatic subjects have been shown to express the low-affinity receptor for IgE on their surface. In this report we demonstrate, using bronchial biopsies, that bronchial epithelial cells of some asthmatic subjects express both the alpha and gamma chains of the high-affinity receptor for IgE (Fcepsilon RI) on their surface and that they are capable of fixing IgE. Second, using reverse transcription-polymerase chain reaction, we show that both control and asthmatic subjects have messenger RNA for Fcepsilon RI. Finally, we demonstrate that this receptor may be functional since stimulation of the cells with the antibody to the alpha chain of Fcepsilon RI results in the liberation of 15-hydroxyeicosatetraenoic acid from epithelial cells of asthmatic, but not control, subjects or subjects suffering from chronic bronchitis. These data suggest that bronchial epithelial cells from at least some asthmatic subjects express a functional high-affinity receptor for IgE and it is therefore possible that these cells may be able to interact directly with inhaled allergens.

ICAM-1 expression in upper respiratory mucosa is differentially related to eosinophil and neutrophil inflammation according to the allergic status

BACKGROUND

Chronic non-infectious sinusitis is an inflammatory disease sharing numerous features with both allergic and non-allergic rhinitis and asthma.

METHODS

In an attempt to analyse the underlying mechanisms of sinus and nasal inflammation, we assessed ICAM-1 immunoreactivity on maxillary sinus, nasal polyp and turbinate biopsies obtained surgically from 21 patients with sinusitis and chronic allergic rhinitis (AR), 23 patients with sinusitis and chronic non-allergic rhinitis (NAR) and 17 non-atopic control subjects. We compared ICAM-1 expression with both eosinophil (EG1) and neutrophil (NP57 elastase) infiltrates.

RESULTS

In nasal turbinates and polyps, ICAM-1 was broadly distributed within the epithelium, on ciliated and basal epithelial cells and in the submucosa on endothelial and inflammatory cells. ICAM-1 was rarely expressed in the mucosa of the sinus, compared with polyps (P < 0.01) and turbinates (P < 0.0001). Submucosal and epithelial eosinophils were increased in both sinus and nasal biopsies from AR by comparison with NAR (P=0.003 and P=0.02) and non-atopic control subjects (P<0.0001 and P=0.014). Submucosal and epithelial neutrophil numbers were increased in the two chronic rhinitis groups and correlated with ICAM-1 submucosal expression in NAR only (P<0.01). On the other hand, epithelial eosinophil numbers correlated with ICAM-1 epithelial expression in AR only (P = 0.002).

CONCLUSION

This study further characterizes sinus and nasal granulocyte inflammation in chronic non-infectious sinusitis and rhinitis and suggests a differential role for ICAM-1 in neutrophil and eosinophil recruitment according to the allergic status.

Expression of cyclo-oxygenase 1 and 2 proteins in upper respiratory mucosa

BACKGROUND

Cyclo-oxygenases 1 (Cox-1) and 2 (Cox-2) catalyse the conversion of arachidonic acid to prostaglandin endoperoxides, leading to the formation of prostaglandin and thromboxane mediators of inflammation. The involvement of these enzymes in inflammatory disorders such as sinusitis and nasal polyps is unknown although this may be relevant to their pathophysiology.

METHODS

We studied Cox-1 and Cox-2 immunoreactivities in nasal polyp, maxillary sinus, and turbinate biopsies obtained from eight patients with chronic allergic rhinitis and sinusitis and/or nasal polyps, 15 patients with chronic non-allergic rhinitis and sinusitis and/or nasal polyps and five control subjects (patients requiring nose surgery not related to sinusitis or nasal polyps).

RESULTS

Both Cox- and Cox-2 were mainly expressed in the epithelium (basal, ciliated) and were found in 16/28 and 25/28 subjects for Cox-1 and Cox-2 respectively. We did not find any differences between the patient populations. There were no correlations between any of the clinical parameters studied nor the pathological patterns and the presence and characteristics of the Cox immunoreactivities.

CONCLUSION

Both cyclo-oxygenase enzymes are expressed in normal human upper respiratory epithelium and are not upregulated in chronic sinusitis nor in nasal polyposis, possibly suggesting that Cox products do not have an important role as mediators of the chronic upper airway inflammation.

Airway inflammation in mild intermittent and in persistent asthma

The severity of asthma can be graded from mild intermittent to severe persistent. Airway inflammation is a feature of persistent asthma. We compared several markers of inflammation in mucosal biopsies and bronchoalveolar lavage fluid (BAL fluid) from 12 healthy control subjects, 24 patients with intermittent asthma, and 18 patients with mild-to-moderate persistent asthma. Epithelial shedding, eosinophil (EG2-positive cells), and activated T-cell (UCHL1) counts in biopsies, and ECP levels in BAL fluids were significantly increased in patients with intermittent asthma by comparison with control subjects and this increase was significantly greater for patients with persistent asthma. Alveolar macrophage activation (percentage of hypodense cells) and the thickness of the basement membrane were significantly increased in asthmatic subjects as compared with controls but there was no difference between the two asthmatic groups. Hyaluronic acid levels in BAL fluids were significantly increased in patients with persistent asthma by comparison with control subjects and patients with intermittent asthma. Mast cell numbers (toluidine blue) in biopsies and histamine or levels in BAL fluids were similar in the three groups. This study shows that airways inflammation is present in patients with intermittent asthma but to a lesser extent than in patients with persistent asthma.

Compositional biases of bacterial genomes and evolutionary implications

We compare and contrast genome-wide compositional biases and distributions of short oligonucleotides across 15 diverse prokaryotes that have substantial genomic sequence collections. These include seven complete genomes (Escherichia coli, Haemophilus influenzae, Mycoplasma genitalium, Mycoplasma pneumoniae, Synechocystis sp. strain PCC6803, Methanococcus jannaschii, and Pyrobaculum aerophilum). A key observation concerns the constancy of the dinucleotide relative abundance profiles over multiple 50-kb disjoint contigs within the same genome. (The profile is rhoXY* = fXY*/fX*fY* for all XY, where fX* denotes the frequency of the nucleotide X and fY* denotes the frequency of the dinucleotide XY, both computed from the sequence concatenated with its inverted complementary sequence.) On the basis of this constancy, we refer to the collection [rhoXY*] as the genome signature. We establish that the differences between [rhoXY*] vectors of 50-kb sample contigs of different genomes virtually always exceed the differences between those of the same genomes. Various di- and tetranucleotide biases are identified. In particular, we find that the dinucleotide CpG=CG is underrepresented in many thermophiles (e.g., M. jannaschii, Sulfolobus sp., and M. thermoautotrophicum) but overrepresented in halobacteria. TA is broadly underrepresented in prokaryotes and eukaryotes, but normal counts appear in Sulfolobus and P. aerophilum sequences. More than for any other bacterial genome, palindromic tetranucleotides are underrepresented in H. influenzae. The M. jannaschii sequence is unprecedented in its extreme underrepresentation of CTAG tetranucleotides and in the anomalous distribution of CTAG sites around the genome. Comparative analysis of numbers of long tetranucleotide microsatellites distinguishes H. influenzae. Dinucleotide relative abundance differences between bacterial sequences are compared. For example, in these assessments of differences, the cyanobacteria Synechocystis, Synechococcus, and Anabaena do not form a coherent group and are as far from each other as general gram-negative sequences are from general gram-positive sequences. The difference of M. jannaschii from low-G+C gram-positive proteobacteria is one-half of the difference from gram-negative proteobacteria. Interpretations and hypotheses center on the role of the genome signature in highlighting similarities and dissimilarities across different classes of prokaryotic species, possible mechanisms underlying the genome signature, the form and level of genome compositional flux, the use of the genome signature as a chronometer of molecular phylogeny, and implications with respect to the three putative eubacterial, archaeal, and eukaryote domains of life and to the origin and early evolution of eukaryotes.

Frequent oligonucleotides and peptides of the Haemophilus influenzae genome

The complete Haemophilus influenzae genome (1.83 Mb, Rd strain) provides opportunities for characterizing global genomic inhomogeneities and for detecting important sequence signals. Along these lines, new methods for identifying frequent words (oligonucleotides and/or peptides) and their distributions are applied to the H.influenzae genome with some comparisons and contrasts made with frequent words of other bacterial genomes. Three major classes of frequent oligonucleotides stand out: (i) oligos related to the familiar uptake signal sequences (USSs), AAGTGCGGT (USS+) and its inverted complement (USS-), (ii) multiple tetranucleotide iterations and (iii) intergenic dyad sequences (ISDs) found as AAGCCCACCCTAC and its dyad form. The USS+ and USS- occur in almost equal counts, are remarkably evenly spaced around the genome, and appear predominantly in the same reading frame of protein coding domains (USS+ translated to Ser-Ala-Val, USS- translated to Thr-Ala-Leu). These observations suggest that USSs contribute to global genomic functions, for example, in replication and/or repair processes, or as membrane attachment sites, or as sequences helping to pack DNA. The long tetranucleotide iterations, virtually unique to H.influenzae (i.e., unknown in other prokaryotes), through polymerase slippage during replication and/or homologous recombination may produce subpopulations expressing alternative proteins. The 13 bp frequent IDS words, invariably intergenic, occur mostly in clusters and provide potential for complex secondary structures suggesting that these sequences may be important signals for regulating the activity of their flanking genes. The frequent oligopeptides of H.influenzae are principally of two kinds--those induced by oligonucleotide frequent words (USSs, tetranucleotide iterations), and those associated with ATP or GTP binding sites that are generally composed of three motifs: the A-box which contributes to delineating the binding pocket; the B-box which functions in hydrolysis; and the C-box whose function is unknown. The A-box occurs fairly universally in prokaryotes and eukaryotes. The B- and C-motifs appear to be specialized to various functional groups (e.g., transport, recombination, chaperone activity). Other putative motifs correspond to homologs of Escherichia coli motifs, for example, are associated with proteins of transcriptional processing, aminoacyl-tRNA synthetases and proteins functioning in electron transfer.

Pathophysiology of allergic rhinitis

Allergy rhinitis results from an IgE-mediated allergy associated with nasal inflammation of variable intensity. The mechanisms of allergic rhinitis have been clarified using nasal challenge with allergen or proinflammatory mediators and measuring cells and mediators released during the early- and late-phase allergic reaction. However, the priming effect of the nasal mucosa is of importance since a single challenge does not perfectly mimic the ongoing allergic reactions induced by repeated allergen exposure. In seasonal and chronic allergic rhinitis, the same cells and mediators are of importance but nonspecific nasal hyperreactivity develops. The regulation of the inflammation of allergic rhinitis is dependent on adhesion molecules and cytokines.

Similarities and dissimilarities of phage genomes

Genomic similarities and contrasts are investigated in a collection of 23 bacteriophages, including phages with temperate, lytic, and parasitic life histories, with varied sequence organizations and with different hosts and with different morphologies. Comparisons use relative abundances of di-, tri-, and tetranucleotides from entire genomes. We highlight several specific findings. (i) As previously shown for cellular genomes, each viral genome has a distinctive signature of short oligonucleotide abundances that pervade the entire genome and distinguish it from other genomes. (ii) The enteric temperate double-stranded (ds) phages, like enterobacteria, exhibit significantly high relative abundances of GpC = GC and significantly low values of TA, but no such extremes exist in ds lytic phages. (iii) The tetranucleotide CTAG is of statistically low relative abundance in most phages. (iv) The DAM methylase site GATC is of statistically low relative abundance in most phages, but not in P1. This difference may relate to controls on replication (e.g., actions of the host SeqA gene product) and to MutH cleavage potential of the Escherichia coli DAM mismatch repair system. (v) The enteric temperate dsDNA phages form a coherent group: they are relatively close to each other and to their bacteria] hosts in average differences of dinucleotide relative abundance values. By contrast, the lytic dsDNA phages do not form a coherent group. This difference may come about because the temperate phages acquire more sequence characteristics of the host because they use the host replication and repair machinery, whereas the analyzed lytic phages are replicated by their own machinery. (vi) The nonenteric temperate phages with mycoplasmal and mycobacterial hosts are relatively close to their respective hosts and relatively distant from any of the enteric hosts and from the other phages. (vii) The single-stranded RNA phages have dinucleotide relative abundance values closest to those for random sequences, presumably attributable to the mutation rates of RNA phages being much greater than those of DNA phages.

Ex vivo pharmacologic modulation of basophil histamine release in asthmatic patients

Histamine is one of a range of mediators which play an important role in asthma, and the "releasability" of basophils has been shown to be upregulated in this disease. In vitro, beta 2-agonists and to a lesser extent corticosteroids have been shown to reduce histamine release. The ex vivo effects of salmeterol and inhaled corticosteroids on histamine release were studied in 78 asthmatic patients with variable disease severity and 20 control subjects. Spontaneous and anti-IgE-induced histamine release was measured in all subjects. Fifteen patients were not receiving any form of treatment, 42 were treated with inhaled corticosteroids, and 21 received inhaled corticosteroids and salmeterol. Seven patients treated with inhaled corticosteroids and seven patients treated with inhaled corticosteroids and salmeterol were tested twice to assess the effect of salmeterol on histamine release. Nine patients treated with inhaled corticosteroids were tested before and after 1 month of salmeterol treatment to determine the possible inhibition by salmeterol. Patients who were treated with inhaled corticosteroids and salmeterol showed significantly lower levels of spontaneous histamine release (median: 2.5%) than untreated (5.2%) and inhaled corticosteroids-treated asthmatics (3.4%). No tachyphylaxis to salmeterol was observed when patients were tested twice at a 3-month interval. This study suggests that salmeterol may have an additive anti-inflammatory effect with inhaled corticosteroids, although this hypothesis must be tested by further studies involving cells obtained by bronchoalveolar lavage and studies with bronchial biopsies.

Inhibition of mediator and cytokine release from dispersed nasal polyp cells by terfenadine

The mechanism of action of H1-blockers requires elucidation because they may possess properties unrelated to the blockage of histamine at its receptor level. A study was performed with enzymatically dispersed cells obtained from nasal polyps to examine the effect of terfenadine (0.1-10 mumol) on the release of leukotrienes (LT) (LTC4/D4 and LTB4) after stimulation by anti-IgE, and on the spontaneous release of cytokines (granulocyte/macrophage-colony stimulating factor [GM-CSF] and tumor necrosis factor-alpha [TNF-alpha]) released from cells cultured for 6 h. Terfenadine inhibited significantly, and in a dose-dependent manner, the release of LTC4/D4, LTB4, TNF-alpha, and GM-CSF. IC50 values were determined for LTC4/D4 (8 mumol), LTB4 (9.9 mumol), TNF-alpha (6.1 mumol), and GM-CSF (4 mumol). Terfenadine was found to possess new antiallergic properties with a novel in vitro model which mimics more closely inflammatory cells of allergic rhinitis or asthma.

Standardization of health assessments for patients aged 75 years and over: 3 years' experience in the Forth Valley Health Board area

BACKGROUND

The new contract for general practitioners (GPs) was introduced in 1990. This required all GPs to offer their patients aged 75 years of over an annual assessment.

AIM

The study aimed to determine if 3 years' experience had resulted in standardization of the way in which health assessments for patients aged 75 years and over are carried out.

METHOD

The study was carried out in 1993. Questionnaires were sent to the principal partners of all 55 general practices in the Forth Valley Health Board (FVHB) area. The main outcome measures were the fulfilment of contractual requirements and standardization of the health assessment process.

RESULTS

Completed questionnaires were returned by 49 practices (89%) Eighty per cent (39 practices) had drawn up their own assessment programme in 1990. Responsibility for assessments was most often (41 practices) shared between different members of the primary care team (84%). Although most practices satisfied contractual requirements, there were wide variations in approach, potentially influencing outcome.

CONCLUSION

Despite three years' experience, no standardized approach to the health assessment of patients aged 75 years and over has been developed. Purchasers of health care require information on the needs of their client population, and this should be available in an accessible, standardized form. There is an urgent need for a review of the way in which the 1990 contract has been implemented to standardize health assessments and improve effectiveness in meeting its original aims.

Different cytokine patterns in bronchial biopsies in asthma and chronic bronchitis

Bronchial biopsies have made possible the detailed study of the pathology of the airways of humans with respiratory disease. Much data has been accumulated on asthmatics or normal controls but much less is known about chronic bronchitics. The aim of this study was to characterize the cellular and cytokine pattern seen in chronic bronchitics and to compare these with control and asthmatic subjects. The patients were also characterized clinically. In this study, immunocytochemistry on cryostat sections from bronchial biopsies were used to determine the level of inflammatory cells and cells of the immune system as well as the pattern of cytokines. This study revealed a distinct cellular and cytokine pattern for each of the three different patient groups, although the diversity of the cytokines analysed was limited by the size of the biopsies. In the inflammatory infiltrate of patients with asthma, CD4+ T-cells and eosinophils were the most prominent cell types discerned. All of the expected cytokines such as IL-1, TNF-alpha, IL-4, IL-5 and IFN-gamma were found. In contrast, the emphasis in chronic bronchitic patients was quite different. The predominant cell types were macrophages, neutrophils, mast cells and CD8+ T-cells, but eosinophils were also abundant. In addition, IL-4 and TNF-alpha were the only cytokines present of those tested.

Stimulation of dispersed nasal polyp cells by hyperosmolar solutions

It has been suggested that hyperosmolarity may be one of the stimuli that provoke exercise-induced asthma and rhinitis. We investigated whether changes in osmolarity could result in increased levels of mediator release from nasal cells. Cells were dispersed from nasal polyps by enzymatic digestion and were incubated for 15 minutes with solutions of varying osmolarity obtained by the addition of mannitol to Hanks' balanced salt solution. After incubation was performed, cell supernatants were removed, and the release of 15-hydroxyeicosatetraenoic acid, prostaglandin2 leukotriene B4, and fibronectin was measured. Lactate dehydrogenase was measured to assess cell viability. Epithelial cells made up 40% to 60% of cells and mononuclear cells 40% to 65%. At 900 mOsm/kg H2O, which has been suggested as the osmolarity of the fluid lining the airways during exercise, we observed a significant increase (Wilcoxon W test) in the release of 15-hydroxyeicosatetraenoic acid (p < 0.008), leukotriene B4 (p < 0.008), and prostaglandin2 (p < 0.008), but no significant increase in the release of fibronectin was seen. No significant increase was seen between lactate dehydrogenase and 15-hydroxyeicosatetraenoic acid release, suggesting that the increase in mediator levels was not caused by cell death. These results show that hyperosmolar solutions can induce activation of nasal cells, which may at least partly explain rhinitis caused by exercise.

Expression and loss of heterozygosity of c-met proto-oncogene in primary breast cancer

The c-met proto-oncogene encodes the receptor to hepatocyte growth factor-scatter factor (HGF-SF), a mesenchyme-derived cytokine with cell-dissociating, invasion, and angiogenic properties. The expression of c-met in breast cancer is the subject of controversy; 111 primary breast cancers were examined for LOH of c-met by Southern blot electrophoresis. c-met expression was measured in a further 40 patients with breast cancer and in 8 patients with benign breast disease by flow cytometry. LOH of c-met was detected in only 4% of informative breast cancers. Expression of c-met was significantly greater in patients with breast cancer than in those with benign breast disease (P < 0.01, Mann-Whitney). There was no correlation however between increased c-met expression and clinicopathological prognostic variables. These results do not support the role of c-met as a tumour suppressor gene in breast cancer but suggest increased receptor expression in malignant breast disease. The significance of this increased expression in breast cancer is the subject of further investigation.

Identification and characterization of a TFIID-like multiprotein complex from Saccharomyces cerevisiae

Although the mechanisms of transcriptional regulation by RNA polymerase II are apparently highly conserved from yeast to man, the identification of a yeast TATA-binding protein (TBP)-TBP-associated factor (TAFII) complex comparable to the metazoan TFIID component of the basal transcriptional machinery has remained elusive. Here, we report the isolation of a yeast TBP-TAFII complex which can mediate transcriptional activation by GAL4-VP16 in a highly purified yeast in vitro transcription system. We have cloned and sequenced the genes encoding four of the multiple yeast TAFII proteins comprising the TBP-TAFII multisubunit complex and find that they are similar at the amino acid level to both human and Drosophila TFIID subunits. Using epitope-tagging and immunoprecipitation experiments, we demonstrate that these genes encode bona fide TAF proteins and show that the yeast TBP-TAFII complex is minimally composed of TBP and seven distinct yTAFII proteins ranging in size from M(r) = 150,000 to M(r) = 25,000. In addition, by constructing null alleles of the cloned TAF-encoding genes, we show that normal function of the TAF-encoding genes is essential for yeast cell viability.

Vascular smooth muscle polyploidy in genetic hypertension: the role of angiotensin II

Flow cytometry DNA analysis has been used to measure the percentage of aortic vascular smooth muscle cells in G2 + M phase of the cell cycle in mature stroke-prone spontaneously hypertensive rats (SHRSP). The effects of three different pharmacological interventions on the cell cycle parameters have also been studied. Vascular smooth muscle cells isolated from SHRSP have significantly elevated G2 + M phase of the cell cycle compared with cells from the normotensive reference strain, Wistar-Kyoto (WKY). This observation reflects an increased tetraploid and octaploid cell populations in vivo. Treatment with a combination of hydralazine and hydrochlorothiazide had no effect on the percentage of cells in G2 + M phase of the cell cycle. Treatments with angiotensin converting enzyme inhibitor, perindopril or AT1 receptor antagonist, losartan, resulted in an equivalent blood pressure-lowering effect to that obtained with hydralazine/hydrochlorothiazide. In contrast to hydralazine/hydrochlorothiazide, these two treatments resulted in a highly significant regression of vascular smooth muscle polyploidy in the SHRSP. We hypothesise that angiotensin II plays an important role in cell cycle regulation in that, alone or in conjunction with one of the inhibitory proteins, it is able to stop the cell cycle progression after endoduplication but before the cytoplasmic division. Pharmacological interventions which remove an excess of angiotensin II may allow the cells to re-enter the cell cycle thus resulting in the regression of vascular smooth muscle polyploidy and improved arterial compliance.

Airways remodelling in asthma: no doubt, no more?

Asthma is a chronic inflammatory disease of the airways invariably associated with healing. Remodelling of the airways can be demonstrated by the activation of airways macrophages, the release of growth factors and fibrogenic cytokines, the activation of fibroblasts and myofibroblast, elastolysis and elastosynthesis, collagen deposition, increased synthesis and release of extracellular matrix components, and an increased mass of smooth muscle and mucous glands. However, the control of remodelling is still poorly understood.

Anaesthesia for caesarean section in a patient with myotonic dystrophy receiving warfarin therapy

A 31-yr-old parturient with myotonic dystrophy and asthma presented for elective Caesarean section. The patient was receiving warfarin having had two previous episodes of thromboembolism. Anticoagulation was subsequently provided by heparin in the weeks prior to delivery. The combination of the patient's medical conditions and the continuing need for anticoagulation presented a considerable anaesthetic problem in planning anaesthesia and analgesia for both elective and emergency delivery. Heparin was discontinued on the day prior to surgery and restarted immediately after surgery. During surgery flowtron anti-embolitic boots were used. Warfarin therapy was recommenced on the seventh postoperative day. Anaesthesia for Caesarean section was provided using a combined spinal epidural technique using a separate needle, separate interspace method. Postoperative pain was relieved by using a continuous epidural infusion, transcutaneous nerve stimulation and diclofenac. No new neurological problems arose despite the use of epidural analgesia in the presence of heparin anticoagulation. This method of providing anaesthesia and postoperative analgesia without the use of opioids in an anticoagulated, asthmatic, myotonic parturient has not been described elsewhere.

Blood monocytes of untreated asthmatics exhibit some features of tissue macrophages

Airway macrophages are activated in asthmatic subjects. Peripheral blood monocytes from these subjects present some functional features of activation, but their membrane markers are not known. Recently a new subtype of blood monocytes, CD14+/CD16+, has been identified which possesses the characteristics of tissue macrophages. A study was carried out on nine normal subjects and 11 untreated asthmatics having variable severities of the disease to examine the phenotypic characteristics of monocytes. CD14, CD16, HLA-DR, CD11a, CD11b, CD44 and CD54 were studied using double fluorescence flow cytometry since these antigens have been defined in the CD14+/CD16+ monocytes. The functional activation of monocytes was examined using the release of superoxide anion. The co-expression of CD14 and CD16 by monocytes in terms of percentage and mean fluorescence intensity was significantly higher in asthmatics (P < 0.002 and P < 0.0001, respectively, Mann-Whitney U-test). There was no difference for the other membrane markers between asthmatics and normal subjects. Superoxide anion release was significantly increased in asthmatic subjects (P < 0.01). This study shows that most blood monocytes of asthmatics are CD14+/CD16+ and are likely to present features of tissue macrophages.

Pharmacologic heterogeneity of human lung and colon cells: effect of terfenadine and cetirizine

H1-blockers may have antiallergic properties which cause the blocking of eicosanoid release, and the effect of these drugs may differ according to the phenotype of mast cells. This study examined the ability of terfenadine and cetirizine to inhibit the release of arachidonic acid-derived mediators from human lung and colon cells. Dispersed cells were challenged with anti-IgE in the presence or absence of 10 microM of terfenadine or cetirizine, and the release of prostaglandin (PG)D2 and leukotriene (LT)C4/D4 was assessed by enzyme immunoassay (EIA). Terfenadine caused significant inhibition of both PGD2 and LTC4/D4 (49 +/- 9 and 29 +/- 19%, respectively) from human lung cells but had a less marked effect on PGD2 release from human colon cells (21 +/- 9% for PGD2 and 18 +/- 9% for LTC4/D4). In contrast, although cetirizine caused significant inhibition of both mediators measured in lung cells (38 +/- 16% for PGD2 and 34 +/- 19% for LTC4), it did not cause any significant inhibition of either mediator from human colon cells. These findings suggest that H1-antagonists may have additional properties, and the differential effects of cetirizine on lung and colon tissue may indicate differences in mast cell phenotype.

Identification and characterization of the type-IVA cyclic AMP-specific phosphodiesterase RD1 as a membrane-bound protein expressed in cerebellum

An antiserum was generated against a dodecapeptide whose sequence is found at the C-terminus of a cyclic AMP (cAMP)-specific, type-IVA phosphodiesterase encoded by the rat 'dunc-like' cyclic AMP phosphodiesterase (RD1) cDNA. This antiserum identified a single approximately 73 kDa protein species upon immunoblotting of cerebellum homogenates. This species co-migrated upon SDS/PAGE with a single immunoreactive species observed in COS cells transfected with the cDNA for RD1. Native RD1 in cerebellum was found to be predominantly (approximately 93%) membrane-associated and could be found in isolated synaptosome populations, in particular those enriched in post-synaptic densities. Fractionation of lysed synaptosomes on sucrose density gradients identified RD1 as co-migrating with the plasma membrane marker 5'-nucleotidase. Laser scanning confocal and digital deconvolution immunofluorescence studies done on intact COS cells transfected with RD1 cDNA showed RD1 to be predominantly localized to plasma membranes but also associated with the Golgi apparatus and intracellular vesicles. RD1-specific antisera immunoprecipitated phosphodiesterase activity from solubilized cerebellum membranes. This activity had the characteristics expected of the type-IV cAMP phosphodiesterase RD1 in that it was cAMP specific, exhibited a low Km cAMP of 2.3 microM, high sensitivity to inhibition by 4-[3-(cyclopentoxyl)-4-methoxyphenyl]-2-pyrrolidone (rolipram) (Ki approximately 0.7 microM) and was unaffected by Ca2+/calmodulin and low concentrations of cyclic GMP. The phosphodiesterase activities of RD1 solubilized from both cerebellum and transfected COS cell membranes showed identical first-order thermal denaturation kinetics at 50 degrees C. Native RD1 from cerebellum was shown to be an integral protein in that it was solubilized using the non-ionic detergent Triton X-100 but not by either re-homogenization or high NaCl concentrations. The observation that hydroxylamine was unable to cause the release of RD1 from either cerebellum or COS membranes and that [3H]palmitate was not incorporated into the RD1 protein immunoprecipitated from COS cells transfected with RD1 cDNA, indicated that RD1 was not anchored by N-terminal acylation. The engineered deletion of the 25 residues forming the unique N-terminal domain of RD1 caused both a profound increase in its activity (approximately 2-fold increase in Vmax) and a profound change in intracellular distribution. Thus, immunofluorescence studies identified the N-terminal truncated species as occurring exclusively ion the cytosol of transfected COS cells. The cDNA for RD1 thus appears to encode a native full-length type-IVA phosphodiesterase that is expressed in cerebellum.(ABSTRACT TRUNCATED AT 400 WORDS)

Inhibitory activity of loratadine and descarboethoxyloratadine on expression of ICAM-1 and HLA-DR by nasal epithelial cells

Nasal epithelial cells represent the first barrier against noxious agents and allergens. In allergic rhinitis, these cells are activated and histamine may be involved in this activation. Loratadine and one of its active metabolites, descarboethoxyloratadine, were studied for their ability to reduce the activation of nasal epithelial cells by histamine. Nasal turbinates or polyps were removed during surgery from 19 subjects, and nasal epithelial cells were recovered after enzymatic digestion. The in vitro activation of epithelial cells with histamine using an optimal dose (1 microM) and an optimal time (24 h) of incubation was studied, and the effect of loratadine or descarboethoxyloratadine (10 microM) was investigated. The expression of membrane markers (intercellular adhesion molecule-1 (ICAM-1) and a human leukocyte class II antigen (HLA-DR) was assessed by immunocytochemical analysis using an alkaline-antialkaline phosphatase (APAAP) system. The spontaneous expression of both markers was not significantly different in cells recovered from nasal turbinates or polyps, and there was a highly significant increase in the numbers of cells expressing ICAM-1 and HLA-DR following incubation with histamine. Loratadine or descarboethoxyloratadine significantly blocked these effects. This study shows a new possible antiallergic effect of H1-blockers and suggests that their effects on epithelial cells may be relevant in vivo.

The effects of perindopril on vascular smooth muscle polyploidy in stroke-prone spontaneously hypertensive rats

OBJECTIVE

To quantify vascular smooth muscle polyploidy and growth kinetics in aortic cells from stroke-prone spontaneously hypertensive rats (SHRSP) and from normotensive Wistar-Kyoto (WKY) rats, and to examine the effects of treatment with the angiotensin converting enzyme (ACE) inhibitor perindopril on these parameters.

DESIGN

The following experimental groups were used: young (age < 20 weeks) and old (age > 20 weeks) untreated WKY rats and untreated SHRSP; SHRSP treated with perindopril, and age- and sex-matched control SHRSP; and SHRSP treated with hydralazine and hydrochlorothiazide and age- and sex-matched control SHRSP. The effects of treatment of the SHRSP with perindopril for 30 days on vascular smooth muscle polyploidy and growth kinetics were measured and compared with the effects of equivalent antihypertensive doses of hydralazine and hydrochlorothiazide.

METHODS

Vascular smooth muscle polyploidy was measured using flow-cytometry DNA analysis of freshly harvested cells. Growth curves were performed on cultured aortic cells. Plasma renin activity was measured by an antibody-trapping method, plasma angiotensin II (Ang II) by radioimmunoassay and plasma ACE activity by a colorimetric method. Cardiac hypertrophy was evaluated by measuring the heart weight:body weight and left ventricle + septum weight:body weight ratios.

RESULTS

The SHRSP had markedly and significantly elevated G2 + M phase of the cell cycle. Treatment with perindopril resulted in a significant reduction in polyploidy in the SHRSP, whereas treatment with hydralazine and hydrochlorothiazide had no effect on the percentage of cells in the G2 + M phase of the cell cycle. The regression of polyploidy after treatment with perindopril was associated with a significant reduction in the concentration of Ang II and ACE activity, and with a significant regression of cardiac hypertrophy. Increased mitogenesis of cultured vascular smooth muscle cells from the SHRSP was not altered by treatment with perindopril.

CONCLUSIONS

ACE inhibition reduces vascular smooth muscle polyploidy in large conduit arteries. This type of vascular protection is mediated by the reduced Ang II and possibly by increased kinins level, rather than by the hypotensive effect alone.

The iso1 gene of Chlamydomonas is involved in sex determination

Sexual differentiation in the heterothallic alga Chlamydomonas reinhardtii is controlled by two mating-type loci, mt+ and mt-, which behave as a pair of alleles but contain different DNA sequences. A mutation in the mt minus-linked imp11 gene has been shown previously to convert a minus gamete into a pseudo-plus gamete that expresses all the plus gametic traits except the few encoded by the mt+ locus. Here we describe the iso1 mutation which is unlinked to the mt- locus but is expressed only in minus gametes (sex-limited expression). A population of minus gametes carrying the iso1 mutation behaves as a mixture of minus and pseudo-plus gametes: the gametes isoagglutinate but they do not fuse to form zygotes. Further analysis reveals that individual gametes express either plus or minus traits: a given cell displays one type of agglutinin (flagellar glycoprotein used for sexual adhesion) and one type of mating structure. The iso1 mutation identifies a gene unlinked to the mating-type locus that is involved in sex determination and the repression of plus-specific genes.

Which bacterium is the ancestor of the animal mitochondrial genome?

We present considerable data supporting the hypothesis that a Sulfolobus- or Mycoplasma-like endosymbiont, rather than an alpha-proteobacterium, is the ancestor of animal mitochondrial genomes. This hypothesis is based on pronounced similarities in oligonucleotide relative abundance extremes common to animal mtDNA, Sulfolobus, and Mycoplasma capricolum and pronounced discrepancies of these relative abundance values with respect to alpha-proteobacteria. In addition, genomic dinucleotide relative abundance measures place Sulfolobus and M. capricolum among the closest to animal mitochondrial genomes, whereas the classical eubacteria, especially the alpha-proteobacteria, are at excessive distances. There are also considerable molecular and cellular phenotypic analogies among mtDNA, Sulfolobus, and M. capricolum.

TFIIF-TAF-RNA polymerase II connection

RNA polymerase transcription factor IIF (TFIIF) is required for initiation at most, if not all, polymerase II promoters. We report here the cloning and sequencing of genes for a yeast protein that is the homolog of mammalian TFIIF. This yeast protein, previously designated factor g, contains two subunits, Tfg1 and Tfg2, both of which are required for transcription, essential for yeast cell viability, and whose sequences exhibit significant similarity to those of the mammalian factor. The yeast protein also contains a third subunit, Tfg3, which is less tightly associated and at most stimulatory to transcription, dispensable for cell viability, and has no known counterpart in mammalian TFIIF. Remarkably, the TFG3 gene encodes yeast TAF30, and furthermore, is identical to ANC1, a gene implicated in actin cytoskeletal function in vivo (Welch and Drubin 1994). Tfg3 is also a component of the recently described mediator complex (Kim et al. 1994), whose interaction with the carboxy-terminal repeat domain of RNA polymerase II enables transcriptional activation. Deletion of TFG3 results in diminished transcription in vivo.

Yeast Taf170 is encoded by MOT1 and exists in a TATA box-binding protein (TBP)-TBP-associated factor complex distinct from transcription factor IID

Our characterization of the Saccharomyces cerevisiae TATA box-binding protein (TBP) has led to the identification of nine specific yeast TBP-associated factors (TAFs) ranging in size from 170 to 25 kDa. The amino acid sequence derived from a purified TAF with an apparent M(r) of 170,000 indicates that yeast Taf170 is encoded by the essential yeast gene MOT1. We describe in this report a series of experiments that demonstrate that the protein encoded by MOT1 is a bona fide yeast TAF and that Taf170 forms a separate complex with TBP distinct from the RNA polymerase II-specific multisubunit transcription factor IID TBP-TAF complex. The significance of this unique TBP-Taf170 complex regarding transcriptional regulation is discussed.

Antithrombotic therapy prescribed for patients with non-rheumatic atrial fibrillation

Patients with non-rheumatic atrial fibrillation have a fivefold increased risk of stroke. Warfarin reduces this risk by approximately two thirds, but evidence for benefit from aspirin is less compelling. We assessed whether our current practice reflects the message of the trials. In a retrospective case record study we reviewed notes of 131 patients with atrial fibrillation (AF), mean age 79 (range 53-95) years, admitted to a medical unit (72) or geriatric assessment unit (59). Thirty-two patients had paroxysmal AF. Of 115 patients with nonrheumatic AF, 36 (31%) had one or more recorded contraindication to anti-coagulation. Although 79 patients (69%) had no recorded contraindication to warfarin, only 2 took warfarin and 15 aspirin prior to admission. Ten patients commenced warfarin and 8 aspirin before discharge. Thirty-nine patients (53%) without contraindication, were discharged without antithrombotic therapy. Despite evidence to support anticoagulating patients with non-rheumatic AF, this rarely occurs.

Low-affinity receptor for IgE on human bronchial epithelial cells in asthma

Bronchial epithelial cells are activated in asthma but the mechanisms underlying this activation are poorly understood. We tested the possibility that bronchial epithelial cells recovered by brushing from 15 asthmatic and 11 control subjects may be activated by an IgE-dependent mechanism. The expression of the low-affinity IgE receptor (CD23) was studied by immunocytochemistry using the alkaline phosphatase anti-alkaline phosphatase technique and immunofluorescence using confocal microscopy. Four of eight allergic asthmatic patients and none of the seven non-allergic asthmatic or control subjects had a positive expression of CD23. The functional activity of CD23 was examined in the cells recovered from these subjects by stimulating them with IgE/anti-IgE. 15-HETE was not released but endothelin was released in the three or four asthmatic patients who had a positive expression of CD23. None of the other subjects released any endothelin. This study suggests that bronchial epithelial cells of asthmatic patients may be directly activated by an IgE-mediated mechanism.

Assessment of inflammation in noninfectious chronic maxillary sinusitis

BACKGROUND AND AIM

Pathologic examination of the sinus mucosa and titration of inflammatory mediators in the sinus fluid were carried out to characterize inflammation in chronic sinusitis and determine whether patients with chronic allergic rhinitis (CAR) and sinusitis differ from patients with chronic nonallergic rhinitis (CNAR) and sinusitis.

METHODS

Nine control subjects (patients requiring ear, nose, and throat surgery not related to sinusitis), 12 patients with CAR and sinusitis, and 13 patients with CNAR and sinusitis were investigated. Eosinophil cationic protein, tryptase, myeloperoxidase, histamine, and prostaglandin D2 were measured in the sinus lavage fluids, and cells were enumerated. The cellular infiltrate was studied by immunohistochemistry with monoclonal antibodies against eosinophil cationic protein (eosinophils), tryptase (mast cells), neutrophil elastase (neutrophils), CD3 (lymphocytes), CD68 (macrophages), and proliferating cell nuclear antigens.

RESULTS

Neutrophils were not increased in sinusitis. In comparison with control subjects, patients with CAR and CNAR with sinusitis showed significant increases in eosinophils and macrophages in biopsy specimens and in eosinophil cationic protein in sinus lavage fluids. In comparison with patients with CNAR, patients with CAR had an increased number of intraepithelial mast cells and lymphocytes.

CONCLUSIONS

These findings suggest that patients with CNAR and sinusitis can be distinguished from patients with CAR and sinusitis, which resembles nonallergic rhinitis with eosinophilia syndrome.

Glu-255 outside the predicted ChvE binding site in VirA is crucial for sugar enhancement of acetosyringone perception by Agrobacterium tumefaciens

Transcriptional activation of the Agrobacterium tumefaciens vir regulon is regulated by phenolics such as acetosyringone (AS), certain monosaccharides, and acidic conditions produced by wounded plant cells. The transmembrane protein VirA acts as an environmental sensor, mediating signal transduction upon perception of these stimuli. Although the periplasmic domain of VirA is not absolutely required for AS-dependent vir gene induction, it is needed for interactions with the periplasmic sugar-binding protein ChvE that result in sugar-induced enhancement of phenolic sensitivity. In this report, we demonstrate that mutations within the periplasmic domain but outside the predicted ChvE binding region can drastically alter the sensitivity of VirA to As. Using site-directed mutagenesis, we have characterized the roles of three individual amino acids in sugar-dependent AS sensitivity and have correlated the induction phenotype with the tumorigenic capacity of strains expressing mutant versions of VirA. Substitution of leucine for Glu-255 abolishes sugar enhancement while replacement with aspartic acid results in a wild-type phenotype. This residue lies outside the predicted ChvE binding site and thus identifies a new region of the VirA periplasmic domain crucial for the enhancement of vir gene induction by carbohydrates. In the absence of inducing sugar, wild-type VirA protein appears to be subject to some form of inhibition that suppresses the maximal level of transcriptional activation; deletions within the periplasmic region relieve this suppression.

Quantification and localization of HLA-DR and intercellular adhesion molecule-1 (ICAM-1) molecules on bronchial epithelial cells of asthmatics using confocal microscopy

An increased expression of HLA-DR and ICAM-1 molecules on bronchial epithelial cells has been observed in asthmatic patients. The aim of this study was to evaluate the localization and to quantify the spontaneous expression of HLA-DR and ICAM-1 on bronchial epithelial cells recovered by bronchial brushing of nine asthmatics and nine controls. Epithelial cells constituted over 95% of cells recovered as shown using an anti-cytokeratin MoAb. Expression of HLA-DR and ICAM-1 was studied using indirect immunofluorescence and confocal microscopy. The intensity of fluorescence of epithelial cells expressing HLA-DR and ICAM-1 was significantly (P < 0.003) increased in asthmatics. In asthmatics, but not in controls, the expression of both molecules was localized in the cytoplasm on the apicolateral portions of the cells. This study shows an up-regulation in the expression of HLA-DR and ICAM-1 molecules by bronchial epithelial cells from asthmatics and a localization of these molecules within the cell.